Quake3World

Green 50% prot 100 max
Yellow 66% prot 150 max
Red 75% prot 200 max

So, when wearing a yellow armor with the value 49, it isn't necessarilly the best choice to pick up a fresh green, resulting in a green armor with the value 99, is it?

Assuming a player received 100 damage, the former receives 34, the latter 50.
This means a player with the health(35-50) with the yellow armor(?-49) should not have picked up fresh green armor, right?

Not quite. Those numbers you state are the damage the armor catches. With that in mind (the result is the actual damage dealt to the player):

100 − 49 * 0.66 = 67.66
100 − 99 * 0.50 = 50.50

That means what matters mostly is the value of armor, not the color, right?
But there should be certainly a criteria whether players should pick up fresh green over the damaged yellow or not.
Even so it won't make any difference in most cases, I guess.